Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening
Abstract
:1. Introduction
Software Name | Type | Description |
---|---|---|
pepATTRACT [37] | Global docking | Web server for blind large-scale peptide–protein docking |
MDockPeP [38] | Global docking | Protein–peptide docking server, that uses ab-initio methods to generate the peptide from sequence and docks it to the receptor structure |
GalaxyPepDock [39] | Template-based | A protein–peptide docking tool based on interaction similarity and energy optimization |
PIPER-FlexPepDock [40] | Global docking | High-resolution peptide–protein docking using a fragment-based approach, that is founded on the Rosseta fragment picker |
CABS-Dock [41] | Global docking | Standalone web server for flexible docking of peptides to proteins without prior knowledge of the binding site |
HPEPDOCK [42] | Global docking | A web server for blind protein–peptide docking through a hierarchical algorithm |
ClusPro PeptiDock [43] | Global docking | A web server for protein–protein docking with efficient global docking of peptide recognition motifs using fast Fourier transform. |
rDock [32] | Local docking | Small molecule docking program, suitable for docking 6–10 amino-acid residue peptides |
CmDock | Local docking | A versatile open source fork of the small molecule docking program rDock, suitable for docking various ligands to proteins and nucleic acids |
ZDOCK server [44] | Global docking | A protein-docking server for the prediction of protein–protein complex structures and symmetric multimers, based on the rigid-body docking programs ZDOCK and M-ZDOCK |
FRODOCK [45] | Global docking | Flexible and fast rotational protein–protein docking |
HawkDock [46] | Global docking | A web server * to predict and analyze a given protein–protein complex based on computational docking using the ATTRACT docking algorithm, the HawkRank scoring function and MM/GBSA free energy decomposition for key amino-acid residues. |
DINC [47] | Local docking | Auto-dock adapted protocol for docking large ligands |
Rosseta FlexPepDock [48] | Global docking | An ab initio approach to simultaneous folding, docking and refinement of peptides onto their receptors |
AutoDock CrankPep [49] | Local docking | Flexible peptide docking to rigid receptors based on folding and docking |
PeptoGrid for AutoDock [50] | Local docking | Rescoring function for AutoDock based on frequency information of ligand atoms |
DynaDock [51] | Local docking | Molecular dynamics based algorithm for flexible protein–peptide docking |
GOLD [52] | Local docking | Docking software based on genetic algorithm for flexible ligand docking |
Surflex [53] | Local docking | Flexible molecular docking software based on a molecular similarity-based search engine |
2. Results
2.1. Library Preparation
2.2. Binding Mode Analysis
3. Discussion
4. Materials and Methods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Jukič, M.; Kralj, S.; Kolarič, A.; Bren, U. Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening. Pharmaceuticals 2023, 16, 1170. https://doi.org/10.3390/ph16081170
Jukič M, Kralj S, Kolarič A, Bren U. Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening. Pharmaceuticals. 2023; 16(8):1170. https://doi.org/10.3390/ph16081170
Chicago/Turabian StyleJukič, Marko, Sebastjan Kralj, Anja Kolarič, and Urban Bren. 2023. "Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening" Pharmaceuticals 16, no. 8: 1170. https://doi.org/10.3390/ph16081170